cogena (version 1.6.2)

enrichment: get the enrichment table from a cogena object.

Description

get the enrichment table from a cogena object with certain clustering methods and number of clusters.

Usage

enrichment(object, method, nCluster, CutoffNumGeneset = Inf, CutoffPVal = 0.05, orderMethod = "max", roundvalue = TRUE, add2 = FALSE)
"enrichment"(object, method, nCluster, CutoffNumGeneset = Inf, CutoffPVal = 0.05, orderMethod = "max", roundvalue = TRUE, add2 = TRUE)

Arguments

object

a genecl or cogena object

method

as clMethods in genecl function

nCluster

as nClust in cogena function.

CutoffNumGeneset

the cut-off of the number of gene sets in the return table

CutoffPVal

the cut-off of p-value. The default is 0.05.

orderMethod

the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.

roundvalue

The default is TRUE. whether or not round the data. such as round(1.54, 1)=1.5

add2

enrichment score for add Up and Down reuglated genes.

Value

a matrix with clusters in row and gene-sets in column.

Details

orderMethod:

• max. ordered by the max value in clusters beside all
• mean. ordered by the mean value in clusters beside all
• All. ordered by all genes
• I. ordered by the I cluster in two clusters (Up or Down-regulated, add2 should be TRUE)
• II. ordered by the II cluster in two clusters (Up or Down-regulated, add2 should be TRUE)
• a character number. like "3".

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v5.0.symbols.gmt.xz", 
package="cogena")

## Not run: 
# genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), 
#     metric="correlation", method="complete", ncore=2, verbose=TRUE)
# 
# clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)
# 
# enrichment.table1 <- enrichment(clen_res, "kmeans", "3")
# enrichment.table2 <- enrichment(clen_res, "kmeans", "3", 
# CutoffNumGeneset=10, orderMethod="mean")
# ## End(Not run)